公开(公告)号：US06341284B1

公开(公告)日：2002-01-22

申请号：US09473318

申请日：1999-12-28

Applicant: Aris Floratos ,  Isidore Rigoutsos ,  B. David Silverman

Inventor： Aris Floratos ,  Isidore Rigoutsos ,  B. David Silverman

IPC: G06F1700

CPC classification number: G06F19/28 ,  G06F17/30539 ,  Y10S707/99936 ,  Y10S707/99942 ,  Y10S707/99943

Abstract: The present invention utilizes a set of D descriptors for each of N items. A value K′ representing a number of descriptors, and a value K for a number of items that should support an hypothesis are generated, preferably via user input. Collections involving K or more items for which there is an association involving a selection of values across at least K′ of the D descriptors are identified, and preferably reported to the user.

Abstract translation: 本发明为N个项目中的每一个使用一组D描述符。 优选地通过用户输入生成表示描述符的数量的值K'，并且生成应该支持假设的项目的数量K。 识别涉及涉及涉及在D描述符的至少K'上选择值的关联的K个或更多个项目的集合，并且优选地向用户报告。

公开(公告)号：US20110237456A1

公开(公告)日：2011-09-29

申请号：US13070884

申请日：2011-03-24

Applicant: Aris FLORATOS ,  Matthew R. NELSON ,  Sally L. JOHN

Inventor： Aris FLORATOS ,  Matthew R. NELSON ,  Sally L. JOHN

IPC: C40B30/04 ,  C12Q1/68 ,  G01N33/48 ,  H01J49/26

CPC classification number: C12Q1/6883 ,  C12Q2600/136 ,  C12Q2600/156 ,  C12Q2600/172 ,  H01J49/00 ,  Y10T436/143333

Abstract: The present invention provides a method for predicting the risk of a patient for developing adverse drug reactions, particularly drug-induced prolonged QT interval or TdP. The invention also provides a method of identifying a subject afflicted with, or at risk of, developing TdP. In some aspects, the methods comprise analyzing at least one genetic marker, wherein the presence of the at least one genetic marker indicates that the subject is afflicted with, or at risk of, developing TdP.

Abstract translation: 本发明提供了一种用于预测患者发展不良药物反应，特别是药物诱导的延长QT间期或TdP的风险的方法。 本发明还提供了鉴定患有TdP或正在发展TdP的受试者的方法。 在一些方面，所述方法包括分析至少一种遗传标记，其中所述至少一种遗传标记的存在表明所述受试者患有或具有发展TdP的风险。

公开(公告)号：US06571199B1

公开(公告)日：2003-05-27

申请号：US09582045

申请日：2000-06-21

Applicant: Aris Floratos ,  Isidore Rigoutsos

Inventor： Aris Floratos ,  Isidore Rigoutsos

IPC: G06F10114

CPC classification number: G06K9/6255 ,  G06F19/22 ,  Y10S707/959 ,  Y10S707/99933 ,  Y10S707/99934 ,  Y10S707/99936 ,  Y10S930/31

Abstract: In a dictionary formation aspect of the invention, a computer-based method of processing a plurality of sequences in a database comprises the following steps. First, the method includes evaluating each of the plurality of sequences including characters which form each sequence. Then, at least one pattern of characters is generated representing at least a subset of the sequences in the database. The pattern has a statistical significance associated therewith, the statistical significance of the pattern being determined by a value representing a minimum number of sequences that the pattern supports in the database.

Abstract translation: 在本发明的词典形成方面，一种在数据库中处理多个序列的基于计算机的方法包括以下步骤。 首先，该方法包括评估多个序列中的每一个，包括形成每个序列的字符。 然后，生成表示数据库中的序列的至少一个子集的至少一个字符模式。 该模式具有与之相关的统计意义，该模式的统计显着性由表示模式在数据库中支持的最小序列数的值确定。

公开(公告)号：US06205444B1

公开(公告)日：2001-03-20

申请号：US09174036

申请日：1998-10-16

Applicant: Aris Floratos ,  Laxmi P. Parida ,  Isidore Rigoutsos

Inventor： Aris Floratos ,  Laxmi P. Parida ,  Isidore Rigoutsos

IPC: G06F1730

CPC classification number: G06F19/22 ,  G06F19/28 ,  Y10S707/99936 ,  Y10S707/99942

Abstract: The method of the present invention aligns a set of N sequences, where N is large. The alignment brings out the best commonality of the N sequences. The method is performed in two stages. A first stage involving discovering motifs, and a second stage involve motif pruning and sequence alignment. The present invention also provides an additional constraint, K, as a user defined control parameter. The additional parameter constrains the alignment of the N sequences to have at least K of the N sequences agree on a character, whenever possible, in the alignment. The alignment number, K, provides a natural constraint for dealing with a large number of sequences in that a commonality across most, if not all sequences is required to be detected.

Abstract translation: 本发明的方法对齐N个序列的集合，其中N大。 对齐提出了N序列的最佳共同性。 该方法分两个阶段进行。 涉及发现基序的第一阶段，第二阶段涉及基序修剪和序列比对。 本发明还提供作为用户定义的控制参数的附加约束K。 附加参数限制了N个序列的对齐，以便在对齐中尽可能地使N个序列的至少K个符合字符。 对齐次数K提供了处理大量序列的自然约束，因为需要检测大多数（如果不是全部）序列的通用性。

公开(公告)号：US20100120049A1

公开(公告)日：2010-05-13

申请号：US12615944

申请日：2009-11-10

Applicant: Aris FLORATOS ,  Sally L. JOHN ,  Matthew R. NELSON

Inventor： Aris FLORATOS ,  Sally L. JOHN ,  Matthew R. NELSON

IPC: C12Q1/68

CPC classification number: C12Q1/6883 ,  C12Q2600/106 ,  C12Q2600/118 ,  C12Q2600/136 ,  C12Q2600/156 ,  C12Q2600/172

Abstract: The present invention provides a method for predicting the risk of a patient for developing adverse drug reactions, particularly Serious Skin Rash (SSR), including such severe adverse reactions such as Stevens-Johnson Syndrome (SJS) and Toxic Epidermal Necrolysis (TEN). The invention also provides a method of identifying a subject afflicted with or at risk of developing SSR. In some aspects, the methods comprise analyzing at least one genetic marker, wherein the presence of the at least one genetic marker indicates that the subject is afflicted with or at risk of developing SSR. Genetic markers useful in accordance with the methods of the invention are disclosed.

Abstract translation: 本发明提供了一种用于预测患者发生不良药物反应，特别是严重皮疹（SSR）的风险的方法，包括诸如史蒂文生 - 约翰逊综合征（SJS）和毒性表皮坏死松解症（TEN）等严重不良反应。 本发明还提供了鉴定患有或有发展SSR风险的受试者的方法。 在一些方面，所述方法包括分析至少一种遗传标记，其中所述至少一种遗传标记的存在表明所述受试者患有或具有发展SSR的风险。 公开了根据本发明方法有用的遗传标记。

公开(公告)号：US20100035265A1

公开(公告)日：2010-02-11

申请号：US12505058

申请日：2009-07-17

Applicant: Aris FLORATOS ,  Sally L. JOHN ,  Matthew Roberts NELSON ,  Ann K. DALY

Inventor： Aris FLORATOS ,  Sally L. JOHN ,  Matthew Roberts NELSON ,  Ann K. DALY

IPC: C12Q1/68

CPC classification number: C12Q1/6883 ,  C12Q2600/106 ,  C12Q2600/136 ,  C12Q2600/142 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/172

Abstract: The present invention provides a method for predicting the risk of a patient for developing adverse drug reactions, particularly Drug-Induced Liver Injury (DILI) or hepatotoxicity. The invention also provides a method of identifying a subject afflicted with, or at risk of, developing DILI. In some aspects, the methods comprise analyzing at least one genetic marker, wherein the presence of the at least one genetic marker indicates that the subject is afflicted with, or at risk of, developing DILI.

Abstract translation: 本发明提供了一种用于预测患者发生不良药物反应，特别是药物诱导性肝损伤（DILI）或肝毒性的风险的方法。 本发明还提供了鉴定患有DILI或正面临其危险的受试者的方法。 在一些方面，所述方法包括分析至少一种遗传标记，其中所述至少一种遗传标记的存在表明所述受试者患有DILI发生或有风险。

公开(公告)号：US06785672B1

公开(公告)日：2004-08-31

申请号：US09582044

申请日：2000-06-21

Applicant: Aris Floratos ,  Isidore Rigoutsos

Inventor： Aris Floratos ,  Isidore Rigoutsos

IPC: G06F1730

CPC classification number: G06K9/6255 ,  G06F19/22 ,  Y10S707/959 ,  Y10S707/99933 ,  Y10S707/99934 ,  Y10S707/99936 ,  Y10S930/31

Abstract: In a sequence homology detection aspect of the invention, a computer-based method of detecting homologies between a plurality of sequences in a database and a query sequence comprises the following steps. First, the method includes accessing patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database. Next, the query sequence is compared to the patterns to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the patterns. Then, a score is generated for each sequence detected to be homologous to the query sequence, wherein the sequence score is based on individual scores generated in accordance with each homologous portion of the sequence detected, and the sequence score represents a degree of homology between the query sequence and the detected sequence.

Abstract translation: 在本发明的序列同源性检测方面，基于计算机的检测数据库中的多个序列与查询序列之间的同源性的方法包括以下步骤。 首先，该方法包括访问与数据库相关联的模式，每个模式表示数据库中的一个或多个序列的至少一部分。 接下来，将查询序列与模式进行比较，以检测查询序列的一个或多个部分是否与由模式表示的数据库的序列的部分同源。 然后，对于检测为与查询序列同源的每个序列产生得分，其中序列分数基于根据检测到的序列的每个同源部分产生的个体得分，并且序列分数表示 查询序列和检测到的序列。

公开(公告)号：US06446011B1

公开(公告)日：2002-09-03

申请号：US09528601

申请日：2000-03-20

Applicant: Aris Floratos ,  Isidore Rigoutsos ,  Gustavo A. Stolovitzky

Inventor： Aris Floratos ,  Isidore Rigoutsos ,  Gustavo A. Stolovitzky

IPC: G01N3348

CPC classification number: G06F19/22 ,  G06F19/24 ,  Y10S707/99936

Abstract: An algorithm which detects tandem repeats (TR) is provided. In an illustrative embodiment, a set of repeating units contained in an input sequence is identified, wherein each given repeating unit satisfies at least the following conditions: (a) a first measure of similarity between adjacent repeating units in the set is greater than a first user defined threshold, and (b) the given repeating unit includes at least one unit having a second measure of similarity with any other unit in the set that is a greater than a second user defined threshold. The method then provides for reporting positions in the input sequence that are covered by the set of repeating units.

Abstract translation: 提供了一种检测串联重复（TR）的算法。 在说明性实施例中，识别包含在输入序列中的一组重复单元，其中每个给定的重复单元至少满足以下条件：（a）该组中相邻重复单元之间的相似度的第一测量值大于第一 用户定义的阈值，以及（b）所述给定的重复单元包括至少一个单元，所述至少一个单元具有与所述集合中的大于第二用户定义的阈值的任何其他单元的相似度的第二度量。 该方法然后提供在输入序列中报告由该组重复单元覆盖的位置。